Publications related to Coding region

Validation of short-pulse reflectometry turbulence measurements with a synthetic diagnostic

Stefano Coda, Stephan Brunner, Oleg Krutkin, Umesh Kumar, Mackenzie Peter-Fulford Van Rossem, Samuele Mazzi

Experimental measurements of the turbulence amplitude utilizing a short pulse reflectometry method are presented. Two discharges with shaped plasma possessing opposite signs of triangularity are considered and a higher turbulence amplitude is found in the ...

IOP Publishing Ltd2024

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Didier Trono, Evaristo Jose Planet Letschert, Wayo Matsushima

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

2024

Statistical learning quantifies transposable element-mediated cis-regulation

Didier Trono, Evaristo Jose Planet Letschert, Julien Léonard Duc, Cyril David Son-Tuyên Pulver, Alexandre Coudray, Julien Paul André Pontis, Delphine Yvette L Grun, Shaoline Sheppard, Raphaël Gérard Théodore Michel Marie de Deloÿe et Fourcade de Fondeville

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

2023

Landscapes of DNA Mechanics and Genomes

Thomas Antonin Zwahlen

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

EPFL2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Live Birth of a Healthy Child in a Couple with Identical mtDNA Carrying a Pathogenic c.471_477delTTTAAAAinsG Variant in the MOCS2 Gene

Konstantin Popadin, Valeriia Timonina

Molybdenum cofactor deficiency type B (MOCODB; #252160) is an autosomal recessive metabolic disorder that has only been described in 37 affected patients. In this report, we describe the presence of an in-frame homozygous variant (c.471_477delTTTAAAAinsG) ...

MDPI2023

Analysis of the influence of errors in DNA-based image coding

Touradj Ebrahimi, Michela Testolina, Davi Nachtigall Lazzarotto

In the last decade, DNA has been increasingly investigated as an alternative medium for cold data storage, presenting several advantages over standard hard drives such as a higher density, longer lifespan and lower energy consumption. However, such coding ...

2023

Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring

Ianina Altshuler

Background Gypsum Hill Spring, located in Nunavut in the Canadian High Arctic, is a rare example of a cold saline spring arising through thick permafrost. It perennially discharges cold (similar to 7 degrees C), hypersaline (7-8% salinity), anoxic (similar ...

BMC2023

Diverse cell-specific patterns of alternative polyadenylation in Drosophila

Bart Deplancke, Sandy Lee

Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs condi ...

Nature Portfolio2022

A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand

Jacques Fellay, Konstantin Popadin, Dmitrii Iliushchenko, Stepan Denisov

The mutational spectrum of the mitochondrial DNA (mtDNA) does not resemble any of the known mutational signatures of the nuclear genome and variation in mtDNA mutational spectra between different organisms is still incomprehensible. Since mitochondria are ...

OXFORD UNIV PRESS2022

Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex

Daniel Constam, Benjamin Marcel Daniel Rothé

Molecular left-right (L-R) asymmetry is established at the node of the mouse embryo as a result of the sensing of a leftward fluid flow by immotile cilia of perinodal crown cells and the consequent degradation of Dand5 mRNA on the left side. We here examin ...

Nature Portfolio2021

Toward a mechanistic understanding of variable chromatin modules

Gerard Llimos Aubach

Our genome is a long sequence of DNA that contains all the information to be able to constitute a living organism like us, similarly to what the letters in a book do to create a story. This sequence, which is a stretch of molecules called nucleotides, is a ...

EPFL2021

Pharmacological characterization of mutant huntingtin aggregate-directed PET imaging tracer candidates

Hilal Lashuel, Anass Chiki

Huntington's disease (HD) is caused by a CAG trinucleotide repeat expansion in the first exon of the huntingtin (HTT) gene coding for the huntingtin (HTT) protein. The misfolding and consequential aggregation of CAG-expanded mutant HTT (mHTT) underpin HD p ...

Nature Portfolio2021

Blind killing of both male and female Drosophila embryos by a natural variant of the endosymbiotic bacterium Spiroplasma poulsonii

Bruno Lemaitre, Samuel Rommelaere, Florent François Masson, Juan Camilo Paredes Escobar, Mario Gonzalo Garcia Arraez

Spiroplasma poulsonii is a vertically transmitted endosymbiont of Drosophila melanogaster that causes male-killing, that is the death of infected male embryos during embryogenesis. Here, we report a natural variant of S. poulsonii that is efficiently verti ...

WILEY2020

Enteric infection induces Lark-mediated intron retention at the 5 ' end of Drosophila genes

Bart Deplancke, Maroun Bou Sleiman, Michael Vincent Frochaux, Dani Osman, Tommaso Andreani

Background RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study ...

2020

Skeletal muscle enhancer interactions identify genes controlling whole-body metabolism

Johan Auwerx, Martin Rainer Wohlwend

Obesity and type 2 diabetes (T2D) are metabolic disorders influenced by lifestyle and genetic factors that are characterized by insulin resistance in skeletal muscle, a prominent site of glucose disposal. Numerous genetic variants have been associated with ...

Nature Research2020

LPA1 receptor and chronic stress: Effects on behaviour and the genes involved in the hippocampal excitatory/inhibitory balance

Maria del Carmen Sandi Perez, Olivia Zanoletti, Alexandre Claude Gustave Bacq, Roman Moreno Fernandez

The LPA1 receptor, one of the six characterized G protein-coupled receptors (LPA1–6) through which lysophosphatidic acid acts, is likely involved in promoting normal emotional behaviours. Current data suggest that the LPA-LPA1-receptor pathway may be invol ...

2020

Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs

Fabrice Daniel Darbellay, Anamaria Necsulea

The functionality of long noncoding RNAs (lncRNAs) is disputed. In general, lncRNAs are under weak selective pressures, suggesting that the majority of lncRNAs may be nonfunctional. However, although some surveys showed negligible phenotypic effects upon l ...

OXFORD UNIV PRESS2020

Hybrid Transcriptional Regulators for the Screening of Target DNA Motifs in Organohalide-Respiring Bacteria

Christof Holliger, Julien Maillard, Mathilde Stéphanie Willemin, Marie Vingerhoets

The bioremediation of persistent organohalide molecules under anoxic conditions mostly relies on the bacterial process called organohalide respiration (OHR). Organohalide-respiring bacteria (OHRB) are phylogenetically diverse anaerobic bacteria that share ...

Frontiers Media SA2020

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Vassily Hatzimanikatis, Pierre Guy Rémy Salvy

Systems biology has long been interested in models capturing both metabolism and expression in a cell. We propose here an implementation of the metabolism and expression model formalism (ME-models), which we call ETFL, for Expression and Thermodynamics Flu ...

Nature Research2020